Physiological response parameters were assessed using mixed-effects linear models across species and treatments. Model selection was carried out using backward elimination of random-effects followed by fixed-effects using the package lmerTest (version 3.1.3)
While value ~ species + fpco2 + ftemp + (1 | colony) + species:ftemp was the best-fit model structure identified, we wanted to model both pCO2 and temperature responses by species so moving forward we are using the following model structure:
value ~ species * (fpco2 + ftemp) + (1 | colony)
Figure:
While value ~ species + ftemp was the best-fit model structure identified, we wanted to model responses with a random effect of colony so moving forward we are using the following model structure:
value ~ species * (fpco2 + ftemp) + (1 | colony)
Figure:
While value ~ species + ftemp + reef + species:ftemp + species:reef was the best-fit model structure identified, we wanted to model both pCO2 and temperature responses by species and with random effect of colony so moving forward we are using the following model structure:
value ~ species * (fpco2 + ftemp) + reef + species:reef + (1 | colony)
Figure:
While value ~ species + fpco2 + ftemp + reef + (1 | colony) + species:fpco2 + species:ftemp + fpco2:ftemp + species:reef + fpco2:reef + ftemp:reef + species:fpco2:ftemp + species:fpco2:reef + species:ftemp:reef + fpco2:ftemp:reef + species:fpco2:ftemp:reef was the best-fit model structure identified, we wanted to model both pCO2 and temperature responses by species and with random effect of colony so moving forward we are using the following model structure:
value ~ species * (fpco2 + ftemp) + reef + species:reef + (1 | colony)
Figure:
Since the best-fit model fits our design, we will proceed with the following model structure:
value ~ species + fpco2 + ftemp + reef + (1 | colony) + species:fpco2 + species:ftemp + fpco2:ftemp + species:reef
Figure:
Since the best-fit model fits our design, we will proceed with the following model structure:
value ~ species + fpco2 + ftemp + reef + (1 | colony) + species:fpco2 + species:ftemp + species:reef + fpco2:reef + species:fpco2:reef
Figure:
This is the same model from Bove et al 2019, just matching aesthetics for this manuscript.
Figure 1. Modeled 95% confidence interval of (A) total host energy reserves (mg cm-2), (B) cell density (106 cells cm-2), and (C) Chlorophyll a (ug cm-2) for S. siderea, P. strigosa, and P. astreoides at T0 (green) or T90 (red/blue), with individual coral fragment physiology denoted by points. Blue denotes 28°C and red denotes 31°C, with pCO2 treatment along the x axis.
Here, I am exploring the relationships between each physiology parameter measured above.
Figure 2. Correlation matrix for S. siderea, P. strigosa, and P. astreoides depicting pair-wise comparisons of physiological parameters within each species. Colour and ellipse width denote R2 of each significant comparison, and blank grids represent non-significant pair-wise comparisons (P > 0.05).Each parameter is denoted in blue text along the diagonal of each plot. Correlations with R2 above 0.5 (shown in orange and red in matrix plot) are explored further below.
##
## Call:
## adonis(formula = value ~ reef + ftemp + fpco2, data = s_df_l, method = "eu")
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## reef 1 544 544.0 0.3565 0.00068 0.553
## ftemp 1 3538 3537.7 2.3184 0.00443 0.126
## fpco2 3 15517 5172.4 3.3897 0.01945 0.012 *
## Residuals 510 778211 1525.9 0.97543
## Total 515 797810 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Call:
## adonis(formula = value ~ reef + ftemp + fpco2, data = p_df_l, method = "eu")
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## reef 1 10809 10809.2 3.4558 0.00709 0.058 .
## ftemp 1 18776 18775.5 6.0027 0.01231 0.014 *
## fpco2 3 31998 10666.2 3.4100 0.02098 0.022 *
## Residuals 468 1463839 3127.9 0.95963
## Total 473 1525422 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Call:
## adonis(formula = value ~ reef + ftemp + fpco2, data = a_df_l, method = "eu")
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## reef 1 78 78.2 0.0742 0.00018 0.790
## ftemp 1 5023 5023.4 4.7659 0.01140 0.025 *
## fpco2 3 11786 3928.7 3.7273 0.02675 0.009 **
## Residuals 402 423715 1054.0 0.96167
## Total 407 440603 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
aov(distance ~ pCO2 * temperature * reef)
## Df Sum Sq Mean Sq F value Pr(>F)
## fpco2 3 52.34 17.447 12.398 1.36e-06 ***
## ftemp 1 4.62 4.620 3.283 0.074304 .
## reef 1 17.19 17.194 12.218 0.000826 ***
## fpco2:ftemp 3 19.90 6.635 4.715 0.004696 **
## fpco2:reef 3 10.08 3.361 2.388 0.076194 .
## ftemp:reef 1 0.68 0.679 0.482 0.489638
## fpco2:ftemp:reef 3 4.93 1.643 1.168 0.328330
## Residuals 70 98.51 1.407
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Reef environment:
## diff lwr upr p adj
## N-F -0.8918785 -1.402693 -0.381064 0.0008610358
Temperature:
## diff lwr upr p adj
## 31-28 0.4629949 -0.04781959 0.9738094 0.07494486
pCO2:
## diff lwr upr p adj
## 420-300 -1.04810665 -2.05630773 -0.03990557 3.852069e-02
## 680-300 -0.09048749 -1.08908913 0.90811415 9.951844e-01
## 3300-300 1.07998914 0.09026878 2.06970950 2.705280e-02
## 680-420 0.95761916 0.02655061 1.88868771 4.147164e-02
## 3300-420 2.12809579 1.20655914 3.04963244 3.394696e-07
## 3300-680 1.17047663 0.25945215 2.08150111 6.360085e-03
aov(distance ~ pCO2 + temperature + reef + pCO2:temperature)
## Df Sum Sq Mean Sq F value Pr(>F)
## fpco2 3 11.91 3.971 2.066 0.1126
## ftemp 1 3.54 3.539 1.841 0.1792
## reef 1 3.00 2.999 1.560 0.2158
## fpco2:ftemp 3 22.06 7.353 3.825 0.0135 *
## Residuals 70 134.57 1.922
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Reef environment:
## diff lwr upr p adj
## N-F 0.3966685 -0.2371093 1.030446 0.2160887
Temperature:
## diff lwr upr p adj
## 31-28 0.4365546 -0.2089166 1.082026 0.1817144
pCO2:
## diff lwr upr p adj
## 420-300 -1.268832 -2.6342004 0.09653637 0.07787008
## 680-300 -0.186533 -1.2666855 0.89361956 0.96853921
## 3300-300 -0.318319 -1.3726392 0.73600121 0.85665896
## 680-420 1.082299 -0.3197300 2.48432814 0.18635502
## 3300-420 0.950513 -0.4317124 2.33273847 0.27742695
## 3300-680 -0.131786 -1.2331696 0.96959758 0.98909261
aov(distance ~ pCO2 + temperature + reef)
## Df Sum Sq Mean Sq F value Pr(>F)
## fpco2 3 32.12 10.707 7.776 0.000173 ***
## ftemp 1 9.68 9.676 7.027 0.010177 *
## reef 1 1.35 1.353 0.983 0.325427
## Residuals 62 85.37 1.377
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Reef environment:
## diff lwr upr p adj
## N-F 0.2780969 -0.2947748 0.8509686 0.3356237
Temperature:
## diff lwr upr p adj
## 31-28 0.7811527 0.1859322 1.376373 0.01094389
pCO2:
## diff lwr upr p adj
## 420-300 -1.36493076 -2.4275070 -0.3023545 0.0065068409
## 680-300 0.01915618 -1.0285582 1.0668705 0.9999591525
## 3300-300 0.48643513 -0.5926162 1.5654864 0.6353107458
## 680-420 1.38408693 0.3363726 2.4318013 0.0048748389
## 3300-420 1.85136589 0.7723146 2.9304172 0.0001582493
## 3300-680 0.46727895 -0.5971405 1.5316984 0.6546745575
##
## Call:
## adonis(formula = value ~ treat2, data = s_plast_l, method = "eu")
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## treat2 8 28005 3500.6 2.1277 0.03488 0.035 *
## Residuals 471 774911 1645.2 0.96512
## Total 479 802916 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Df Sum Sq Mean Sq F value Pr(>F)
## treat2 8 44.96 5.620 4.859 5.79e-05 ***
## reef 1 3.94 3.937 3.404 0.0685 .
## Residuals 86 99.47 1.157
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Call:
## adonis(formula = value ~ treat2, data = p_plast_l, method = "eu")
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## treat2 8 65917 8239.6 2.384 0.04285 0.026 *
## Residuals 426 1472357 3456.2 0.95715
## Total 434 1538274 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Df Sum Sq Mean Sq F value Pr(>F)
## treat2 8 31.61 3.951 3.491 0.00173 **
## reef 1 9.92 9.916 8.763 0.00408 **
## Residuals 77 87.13 1.132
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Call:
## adonis(formula = value ~ treat2, data = a_plast_l, method = "eu")
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## treat2 8 32081 4010.1 3.6221 0.069 0.003 **
## Residuals 391 432883 1107.1 0.931
## Total 399 464964 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Df Sum Sq Mean Sq F value Pr(>F)
## treat2 8 83.07 10.384 12.94 3.03e-11 ***
## reef 1 8.66 8.656 10.78 0.0016 **
## Residuals 70 56.19 0.803
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| treatment | N | mean | lower 95% | upper 95% |
|---|---|---|---|---|
| (a) SSID | ||||
| 288_28 | 11 | 0.49 | 0.40 | 0.57 |
| 311_31 | 9 | 0.44 | 0.35 | 0.52 |
| 3285_28 | 12 | 0.45 | 0.37 | 0.53 |
| 3309_31 | 12 | 0.39 | 0.31 | 0.47 |
| 405_31 | 12 | 0.46 | 0.38 | 0.54 |
| 447_28 | 12 | 0.52 | 0.44 | 0.60 |
| 673_28 | 13 | 0.47 | 0.38 | 0.54 |
| 701_31 | 12 | 0.41 | 0.33 | 0.49 |
| (b) PSTR | ||||
| 288_28 | 16 | 0.56 | 0.49 | 0.64 |
| 311_31 | 9 | 0.32 | 0.23 | 0.41 |
| 3285_28 | 16 | 0.42 | 0.34 | 0.50 |
| 3309_31 | 8 | 0.17 | 0.08 | 0.27 |
| 405_31 | 6 | 0.18 | 0.07 | 0.29 |
| 447_28 | 5 | 0.42 | 0.30 | 0.54 |
| 673_28 | 14 | 0.45 | 0.37 | 0.53 |
| 701_31 | 7 | 0.21 | 0.11 | 0.31 |
| (c) PAST | ||||
| 288_28 | 11 | 0.24 | 0.15 | 0.33 |
| 311_31 | 6 | 0.19 | 0.08 | 0.29 |
| 3285_28 | 12 | 0.11 | 0.02 | 0.20 |
| 3309_31 | 4 | 0.06 | -0.05 | 0.17 |
| 405_31 | 7 | 0.16 | 0.07 | 0.27 |
| 447_28 | 12 | 0.21 | 0.12 | 0.30 |
| 673_28 | 10 | 0.15 | 0.06 | 0.25 |
| 701_31 | 9 | 0.11 | 0.01 | 0.20 |
| treatment | N | mean | lower 95% | upper 95% |
|---|---|---|---|---|
| (a) SSID | ||||
| 288_28 | 11 | 0.40 | 0.29 | 0.50 |
| 311_31 | 9 | 0.37 | 0.26 | 0.48 |
| 3285_28 | 12 | 0.37 | 0.27 | 0.47 |
| 3309_31 | 12 | 0.35 | 0.25 | 0.45 |
| 405_31 | 12 | 0.38 | 0.29 | 0.48 |
| 447_28 | 12 | 0.41 | 0.30 | 0.51 |
| 673_28 | 13 | 0.33 | 0.23 | 0.43 |
| 701_31 | 12 | 0.31 | 0.21 | 0.41 |
| (b) PSTR | ||||
| 288_28 | 16 | 0.27 | 0.18 | 0.37 |
| 311_31 | 9 | 0.14 | 0.02 | 0.24 |
| 3285_28 | 15 | 0.22 | 0.12 | 0.32 |
| 3309_31 | 8 | 0.08 | -0.04 | 0.19 |
| 405_31 | 5 | 0.12 | -0.03 | 0.26 |
| 447_28 | 5 | 0.26 | 0.11 | 0.40 |
| 673_28 | 14 | 0.22 | 0.11 | 0.32 |
| 701_31 | 7 | 0.07 | -0.04 | 0.20 |
| (c) PAST | ||||
| 288_28 | 11 | 0.21 | 0.10 | 0.33 |
| 311_31 | 6 | 0.26 | 0.13 | 0.38 |
| 3285_28 | 12 | 0.13 | 0.01 | 0.24 |
| 3309_31 | 4 | 0.20 | 0.07 | 0.33 |
| 405_31 | 7 | 0.22 | 0.10 | 0.34 |
| 447_28 | 12 | 0.17 | 0.06 | 0.27 |
| 673_28 | 10 | 0.11 | 0.01 | 0.23 |
| 701_31 | 9 | 0.16 | 0.05 | 0.28 |
| treatment | N | mean | lower 95% | upper 95% |
|---|---|---|---|---|
| (a) SSID | ||||
| 288_28 | 11 | 1.15 | 0.95 | 1.35 |
| 311_31 | 8 | 0.82 | 0.61 | 1.02 |
| 3285_28 | 12 | 1.10 | 0.91 | 1.29 |
| 3309_31 | 12 | 0.77 | 0.60 | 0.96 |
| 405_31 | 12 | 0.75 | 0.57 | 0.94 |
| 447_28 | 12 | 1.08 | 0.90 | 1.26 |
| 673_28 | 13 | 1.27 | 1.10 | 1.45 |
| 701_31 | 12 | 0.94 | 0.75 | 1.11 |
| (b) PSTR | ||||
| 288_28 | 16 | 0.77 | 0.60 | 0.93 |
| 311_31 | 9 | 0.50 | 0.30 | 0.68 |
| 3285_28 | 16 | 0.62 | 0.45 | 0.78 |
| 3309_31 | 8 | 0.34 | 0.15 | 0.55 |
| 405_31 | 6 | 0.40 | 0.16 | 0.65 |
| 447_28 | 5 | 0.67 | 0.41 | 0.92 |
| 673_28 | 14 | 0.56 | 0.37 | 0.75 |
| 701_31 | 7 | 0.29 | 0.07 | 0.51 |
| (c) PAST | ||||
| 288_28 | 11 | 0.82 | 0.61 | 1.03 |
| 311_31 | 6 | 0.65 | 0.41 | 0.88 |
| 3285_28 | 12 | 0.58 | 0.38 | 0.78 |
| 3309_31 | 4 | 0.41 | 0.16 | 0.65 |
| 405_31 | 7 | 0.73 | 0.51 | 0.95 |
| 447_28 | 12 | 0.90 | 0.71 | 1.10 |
| 673_28 | 10 | 0.61 | 0.41 | 0.81 |
| 701_31 | 9 | 0.43 | 0.23 | 0.64 |
| treatment | N | mean | lower 95% | upper 95% |
|---|---|---|---|---|
| (a) SSID | ||||
| 288_28 | 11 | 3.32 | 2.23 | 4.46 |
| 311_31 | 9 | 2.45 | 1.33 | 3.58 |
| 3285_28 | 12 | 2.04 | 0.97 | 3.07 |
| 3309_31 | 12 | 1.18 | 0.12 | 2.23 |
| 405_31 | 12 | 2.61 | 1.55 | 3.67 |
| 447_28 | 12 | 3.48 | 2.42 | 4.50 |
| 673_28 | 13 | 2.96 | 1.95 | 3.98 |
| 701_31 | 12 | 2.10 | 1.04 | 3.14 |
| (b) PSTR | ||||
| 288_28 | 16 | 2.16 | 1.14 | 3.15 |
| 311_31 | 9 | 0.42 | -0.77 | 1.60 |
| 3285_28 | 16 | 1.53 | 0.53 | 2.52 |
| 3309_31 | 8 | -0.27 | -1.48 | 0.89 |
| 405_31 | 6 | 0.45 | -0.96 | 1.86 |
| 447_28 | 5 | 2.16 | 0.75 | 3.61 |
| 673_28 | 14 | 1.71 | 0.68 | 2.75 |
| 701_31 | 7 | -0.09 | -1.30 | 1.14 |
| (c) PAST | ||||
| 288_28 | 11 | 7.29 | 6.13 | 8.48 |
| 311_31 | 6 | 6.42 | 5.02 | 7.74 |
| 3285_28 | 12 | 5.92 | 4.74 | 7.16 |
| 3309_31 | 4 | 4.86 | 3.51 | 6.15 |
| 405_31 | 6 | 5.51 | 4.22 | 6.83 |
| 447_28 | 12 | 6.43 | 5.28 | 7.57 |
| 673_28 | 10 | 5.09 | 3.84 | 6.35 |
| 701_31 | 8 | 4.19 | 2.87 | 5.45 |
| treatment | N | mean | lower 95% | upper 95% |
|---|---|---|---|---|
| (a) SSID | ||||
| 288_28 | 11 | 111.62 | 79.83 | 142.93 |
| 311_31 | 9 | 105.32 | 71.66 | 138.94 |
| 3285_28 | 12 | 48.77 | 17.98 | 79.06 |
| 3309_31 | 12 | 32.88 | 2.52 | 62.85 |
| 405_31 | 12 | 78.09 | 46.98 | 108.90 |
| 447_28 | 12 | 155.02 | 123.15 | 185.60 |
| 673_28 | 13 | 83.80 | 54.26 | 112.09 |
| 701_31 | 12 | 82.13 | 52.64 | 112.24 |
| (b) PSTR | ||||
| 288_28 | 16 | 186.56 | 157.46 | 214.70 |
| 311_31 | 9 | 120.87 | 86.12 | 156.21 |
| 3285_28 | 16 | 78.92 | 50.45 | 107.95 |
| 3309_31 | 8 | -1.60 | -37.38 | 34.54 |
| 405_31 | 6 | 26.31 | -13.62 | 66.76 |
| 447_28 | 5 | 161.10 | 118.69 | 203.66 |
| 673_28 | 14 | 83.70 | 54.83 | 112.50 |
| 701_31 | 7 | 17.80 | -17.46 | 55.99 |
| (c) PAST | ||||
| 288_28 | 11 | 96.99 | 64.84 | 130.13 |
| 311_31 | 6 | 155.80 | 116.69 | 193.74 |
| 3285_28 | 12 | 15.60 | -16.92 | 47.45 |
| 3309_31 | 4 | 61.57 | 19.84 | 101.90 |
| 405_31 | 7 | 52.42 | 15.21 | 88.19 |
| 447_28 | 12 | 64.58 | 33.39 | 95.25 |
| 673_28 | 10 | 33.03 | -0.94 | 66.96 |
| 701_31 | 9 | 95.56 | 61.63 | 129.07 |
| treatment | N | mean | lower 95% | upper 95% |
|---|---|---|---|---|
| (a) SSID | ||||
| 288_28 | 11 | 2.02 | 1.62 | 2.42 |
| 311_31 | 8 | 1.62 | 1.21 | 2.03 |
| 3285_28 | 12 | 1.92 | 1.56 | 2.28 |
| 3309_31 | 12 | 1.53 | 1.18 | 1.88 |
| 405_31 | 12 | 1.58 | 1.21 | 1.95 |
| 447_28 | 12 | 2.03 | 1.66 | 2.40 |
| 673_28 | 13 | 2.06 | 1.71 | 2.42 |
| 701_31 | 12 | 1.66 | 1.29 | 2.01 |
| (b) PSTR | ||||
| 288_28 | 16 | 1.59 | 1.25 | 1.93 |
| 311_31 | 9 | 0.96 | 0.58 | 1.33 |
| 3285_28 | 15 | 1.27 | 0.90 | 1.62 |
| 3309_31 | 8 | 0.60 | 0.22 | 0.98 |
| 405_31 | 5 | 0.71 | 0.17 | 1.27 |
| 447_28 | 5 | 1.38 | 0.83 | 1.95 |
| 673_28 | 14 | 1.23 | 0.86 | 1.62 |
| 701_31 | 7 | 0.56 | 0.16 | 0.97 |
| (c) PAST | ||||
| 288_28 | 11 | 1.26 | 0.83 | 1.68 |
| 311_31 | 6 | 1.12 | 0.66 | 1.58 |
| 3285_28 | 12 | 0.86 | 0.42 | 1.30 |
| 3309_31 | 4 | 0.56 | 0.14 | 0.97 |
| 405_31 | 7 | 1.13 | 0.71 | 1.56 |
| 447_28 | 12 | 1.26 | 0.85 | 1.67 |
| 673_28 | 10 | 0.85 | 0.43 | 1.27 |
| 701_31 | 9 | 0.73 | 0.31 | 1.14 |
Session information from the last run date on 2020-11-18:
## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] wesanderson_0.3.6 RColorBrewer_1.1-2 gridGraphics_0.5-0
## [4] corrplot_0.84 Hmisc_4.2-0 Formula_1.2-3
## [7] survival_2.44-1.1 magick_2.2 ggpubr_0.2.4
## [10] magrittr_1.5 vroom_1.2.0 lmerTest_3.1-3
## [13] lme4_1.1-21 Matrix_1.2-17 kableExtra_1.1.0
## [16] ggfortify_0.4.7 cowplot_1.0.0 Rmisc_1.5
## [19] shiny_1.4.0 vegan_2.5-5 lattice_0.20-41
## [22] permute_0.9-5 forcats_0.4.0 stringr_1.4.0
## [25] purrr_0.3.3 tibble_2.1.3 tidyverse_1.3.0
## [28] plotly_4.9.0 openxlsx_4.1.2 tidyr_1.0.0
## [31] ggbiplot_0.55 scales_1.1.0 plyr_1.8.5
## [34] dplyr_0.8.3 ggplot2_3.2.1 readr_1.3.1
## [37] knitr_1.25
##
## loaded via a namespace (and not attached):
## [1] minqa_1.2.4 colorspace_1.4-1 ggsignif_0.6.0
## [4] ellipsis_0.3.0 htmlTable_1.13.1 base64enc_0.1-3
## [7] fs_1.3.1 rstudioapi_0.10 farver_2.0.1
## [10] ggrepel_0.8.1 bit64_0.9-7 fansi_0.4.1
## [13] lubridate_1.7.4 xml2_1.2.2 splines_3.5.1
## [16] jsonlite_1.6 nloptr_1.2.1 broom_0.5.2
## [19] cluster_2.1.0 dbplyr_1.4.2 compiler_3.5.1
## [22] httr_1.4.1 backports_1.1.5 assertthat_0.2.1
## [25] fastmap_1.0.1 lazyeval_0.2.2 cli_2.0.1
## [28] later_1.0.0 acepack_1.4.1 htmltools_0.4.0
## [31] tools_3.5.1 gtable_0.3.0 glue_1.3.1
## [34] Rcpp_1.0.3 cellranger_1.1.0 vctrs_0.2.4
## [37] nlme_3.1-140 xfun_0.8 rvest_0.3.5
## [40] mime_0.7 lifecycle_0.2.0 MASS_7.3-51.4
## [43] hms_0.5.3 promises_1.1.0 parallel_3.5.1
## [46] yaml_2.2.0 gridExtra_2.3 rpart_4.1-15
## [49] latticeExtra_0.6-28 stringi_1.4.5 highr_0.8
## [52] checkmate_1.9.4 boot_1.3-23 zip_2.0.3
## [55] rlang_0.4.5 pkgconfig_2.0.3 evaluate_0.14
## [58] labeling_0.3 htmlwidgets_1.3 bit_1.1-14
## [61] tidyselect_1.0.0 R6_2.4.1 generics_0.0.2
## [64] DBI_1.0.0 pillar_1.4.3 haven_2.2.0
## [67] foreign_0.8-71 withr_2.1.2 mgcv_1.8-28
## [70] nnet_7.3-12 modelr_0.1.5 crayon_1.3.4
## [73] rmarkdown_1.16 readxl_1.3.1 data.table_1.12.2
## [76] reprex_0.3.0 digest_0.6.23 webshot_0.5.1
## [79] xtable_1.8-4 httpuv_1.5.2 numDeriv_2016.8-1.1
## [82] munsell_0.5.0 viridisLite_0.3.0